The suspendion design makes alot of differnce. The E34 is a strut suspension on all 4 corners. The E39 is strut in front and shock absorber in rear... meaning different suspension in the back.
Generally speaking ... all strut type suspension will be quite harsh when it comes to bumps... If you got sport suspension strut type, it is pretty downright harsh on massive bump or potholes. If you got regular suspension, it is not so bad... but any strut car will never ride as smooth as traditional suspension type.
The reason for using strut suspension is that it is a much cheaper suspension setup.... engineering, space and parts.
There are always some sort of compromises to all different suspension types.... but BMW has always use strut suspensions.